2.1 Pre-processing
To run MeStudio, a pre-processing python script named ms_replacRhas been implemented to produce consistent formatting on the sequence
identifiers from the genomic annotation, sequencer-produced modified
base calls, and the genomic sequence file. To avoid possible
inconsistencies at the sequence identifiers level (the “seqid” field)
between FASTA and annotation files, we have implemented a quality check
in this regard. More details are provided in the MeStudio manual on
GitHub.